Almost 100 people are now on the waiting list for gender-reassignment surgery, but they face waiting 50 years for the life-changing procedure under Ministry of Health guidelines.

There are 71 people waiting for male to female operations, and 17 on the waitlist for female to male.

Public funding pays for three male-to-female and one female-to-male surgeries every two years, and they have to be performed overseas as there is no one in New Zealand who is able to carry out the procedures.

Jennifer Shields is in the process of getting onto the waiting list for gender reassignment surgery, and said the prospect of waiting half a century is "ridiculous".

"It's absurd, at this rate I wouldn't get the surgery until I was 73.

"I know so many people who aren't even bothering to get on [the list] because there's no point at this rate.

"To even get on the list you have to appointments with a psychiatrist and a psychologist, which pretty much have to come out of your own pocket. It's hundreds and hundreds of dollars, just to get on this list which is at such a slow rate now.

"It's really discouraging, it's just a disappointment."

Shields said when the rates were established in 2003 it may have catered to demand, but this was not the case now.

"With the increase in acceptance and more people coming out, three every two years might have been all right back then but there's so much more that needs to happen now."

"Through the conversations we've been having as a society, people are more aware of it.

"Numbers are rising in surgery but also in mental health services. There's always been the numbers of people with gender issues, but now people are less likely to hide it and are more likely to do something about it.

"[Surgery] is not always the first step, but it's important to have the option."

Duder said Rainbow Youth has had an increase in young gender diverse people going to the organisation for support.

Ministry of Health acting chief medical officer Dr Andrew Simpson said funding for gender reassignment surgery is funded through the High Cost Treatment Pool, with male to female surgeries costing about $35,000-$40,000 and female to male costing as much as $180,000.

He said the number of surgeries will be increased for later this year and into next year.

"Four male to female and one female to male overseas surgeries have been initiated for 2016/17. There will be catch up surgeries once the new system has successfully bedded down, to fulfil the commitment to funding four surgeries every two years."

Since the retirement of the plastic surgeon on the gender reassignment surgery team in 2014, the ministry has been referring people overseas for male to female surgery.

"Female to male surgery is highly specialised surgery and has always been carried out overseas," Simpson said.